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Multilocus Phylogeny Reveals Taxonomic Misidentification of the Schizopora Paradoxa (KUC8140) Representative Genome

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Multilocus Phylogeny Reveals Taxonomic Misidentification of the Schizopora Paradoxa (KUC8140) Representative Genome A peer-reviewed open-access journal MycoKeysMultilocus 38: 121–127 (2018)phylogeny reveals taxonomic misidentification of the Schizopora paradoxa... 121 doi: 10.3897/mycokeys.38.28497 SHORT COMMUNICATION MycoKeys http://mycokeys.pensoft.net Launched to accelerate biodiversity research Multilocus phylogeny reveals taxonomic misidentification of the Schizopora paradoxa (KUC8140) representative genome Javier Fernández-López1, María P. Martín1, Margarita Dueñas1, M. Teresa Telleria1 1 Departmento de Micología, Real Jardín Botánico, RJB-CSIC, Plaza de Murillo 2, 28014 Madrid, Spain Corresponding author: Javier Fernández-López ([email protected]) Academic editor: T. Lumbsch | Received 20 July 2018 | Accepted 13 August 2018 | Published 28 August 2018 Citation: Fernández-López J, Martín MP, Dueñas M, Telleria MT (2018) Multilocus phylogeny reveals taxonomic misidentification of theSchizopora paradoxa (KUC8140) representative genome. MycoKeys 38: 121–127. https://doi. org/10.3897/mycokeys.38.28497 Abstract Schizopora paradoxa, current name Xylodon paradoxus, is a white-rot fungus with certain useful biotechno- logical properties. The representative genome of Schizopora paradoxa strain KUC8140 was published in 2015 as part of the 1000 Fungal Genomes Project. Multilocus phylogenetic analyses, based on three nu- clear regions (ITS, LSU and rpb2), confirmed a misidentification of S. paradoxa strain KUC8140 which should be identified as Xylodon ovisporus. This wrong identification explains the unexpected geographical distribution of S. paradoxa, since this species has a European distribution, whereas the strain KUC8140 was recorded from Korea, Eastern Asia. Keywords Hymenochaetales, phylogenetic analyses, taxonomy, white-rot fungi, Xylodon Introduction The genus Schizopora Velen., currently synonymous with Xylodon (Pers.) Fr. (Riebesehl and Langer 2017), includes white-rot fungi that play an important role in ecosys- tem processes as a wood decomposer. The description and identification of Xylodon (=Schizopora) species, based on morphological characters, has led to inaccuracies due to a lack of clear diagnostic characters and it has been assumed that many Xylodon species have a worldwide distribution (Paulus et al. 2000). However, during the last Copyright Javier Fernández-López et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 122 Javier Fernández-López et al. / MycoKeys 38: 121–127 (2018) decade, it has been pointed out that fungal cosmopolitanism could be the result of the application of a morphological species recognition criterion and not the result of an actual biogeographical pattern (Taylor et al. 2006). Moreover, phylogenetic analyses have revealed an undescribed species diversity masked by the morphological species recognition approach (Taylor et al. 2000). The representative genome of Schizopora paradoxa strain KUC8140, current name Xylodon paradoxus (Schrad.) Chevall., was sequenced in 2015 as part of the 1000 Fun- gal Genomes Project (http://jgi.doe.gov/fungi) (Min et al. 2015); this strain was col- lected from an oak forest in Korea. Usually X. paradoxus has been associated with late stages of wood decay, mainly in deciduous forests and shows useful biotechnological properties for bioremediation, such as tolerance to heavy metals or dye decolourising activity (Lee et al. 2014). It has been recorded around the world; however, available ge- netic data point to a European distribution (Paulus et al. 2000). Within the framework of a broader study of Xylodon through molecular approaches, the taxonomic identity of the strain KUC8140 has been assessed. Materials and methods In order to infer the taxonomic position of the strain KUC8140, phylogenetic rela- tionships of six Xylodon species were addressed. DNA from specimens of X. paradoxus, X. quercinus (Pers.) Gray, X. nothofagi (G. Cunn.) Hjorstam & Ryvarden, X. raduloides Riebesehl & E. Langer, X. flaviporus (Ber. & M.A. Curtis ex Cooke) Riebesehl & E. Langer and X. ovisporus (Corner) Riebesehl & E. Langer was extracted from herbaria specimens and culture collections (Table 1). Three specimens of the sister genusLyo - myces P. Karst. were included as outgroup in the phylogenetic analyses (Table 1). DNA isolation was performed using DNeasy™ Plant Mini Kit (Qiagen, Valencia, California, USA) following the manufacturer’s instructions. Three nuclear regions were amplified and sequenced: nuclear ribosomal internal transcribed spacer (ITS, fungal barcoding; Schoch et al. 2012), nuclear large ribosomal subunit (LSU) and the second largest subunit of RNA polymerase II (rpb2). Direct Polymerase chain reactions (PCRs) were performed to obtain sequences from ITS and LSU with the pair of primers ITS5/ITS4 (White et al. 1990) and LR0R/LR5 (Rehner and Samuels 1994), respectively. Nested- PCRs were done to obtain amplifications of rpb2 fragments, using RPB2-5F/RPB2- 7.1R (Liu et al. 1999, Matheny 2005) for the first amplification followed by RPB2-6F/ RPB2-7R2 (Matheny et al. 2007), using 1 μl of the first PCR as target DNA. Ampli- fications were undertaken using illustra™ PuReTaq™ Ready-To-Go™ PCR beads (GE Healthcare, Buckinghamshire, UK) as described in Winka et al. (1998), following thermal cycling conditions in Martín and Winka (2000). Negative controls lacking fungal DNA were run for each experiment to check for contamination. Amplifications were assayed by gel electrophoresis in 2% Pronadisa D-1 Agarose (Lab. Conda, Tor- rejón de Ardoz, Spain). Amplified DNA fragments were purified from the agarose gel using the Wizard SV Gel and PCR Clean-Up System (Promega Corporation, Madi- son, WI, USA) and sent to Macrogen Korea (Seoul, Korea) for sequencing. Primers, Multilocus phylogeny reveals taxonomic misidentification of the Schizopora paradoxa... 123 Table 1. Specimen information, GenBank accession numbers and genome BLAST searches (ID) used in this study. New sequences generated in this study are indicated in bold. n.d.: no data. GenBank accession number Species Specimen voucher Country ITS LSU rpb2 HHB 10401 USA MH260068 MH260061 MH259316 Lyomyces crustosus HHB 13100 USA MH260069 MH260062 MH259317 UC 2022841 USA KP814310 n.d. n.d. ICMP 13836 Taiwan AF145585 n.d. n.d. Xylodon flaviporus MA-Fungi 79440, 12094IS Germany MH260071 MH260066 MH259319 ICMP 13839 New Zealand AF145582 MH260064 MH259322 Xylodon nothofagi PDD 91630, BCP 3306 New Zealand GQ411524 n.d. n.d. ICMP 13835 Taiwan AF145586 MH260063 MH259320 Xylodon ovisporus ICMP 13837 Taiwan AF145587 n.d. n.d. FCUG 2425 Russia AF145577 n.d. n.d. Xylodon paradoxus MA-Fungi 70444, 11060MD France MH260070 MH260065 n.d. MA-Fungi 81294, 13833MD France MH260072 n.d. MH259318 H 6013352 Finland KT361632 n.d. n.d. Xylodon quercinus MA-Fungi 91311, 1JFL Spain MH260073 MH260067 MH259321 ICMP 13833 Australia AF145580 KY962853 n.d. Xylodon raduloides MA-Fungi 75310, GP2291 Spain KY962825 KY962864 KY967055 Schizopora paradoxa KUC8140 Korea ID14957398 ID14957349 ID1495735 used for sequencing, were those used for PCR amplifications. Additional searches for the six Xylodon species in EMBL/GenBank/DDBJ databases were performed in order to complete the molecular information available for this genus. Using the BLAST tool from the JGI portal, ITS, LSU and rpb2 sequences were extracted from the KUC8140 strain genome (https://genome.jgi.doe.gov/pages/blast- query.jsf?db=Schpa1). The same regions from X. paradoxus specimens FCUG-2425, MA-Fungi 70444 and MA-Fungi 81294 were used as reference sequences for BLAST searches, respectively (Table 1). For ITS and LSU, custom search settings were used (blastn; all databases; Expect = 1*10-3; Word size = 11; Filter low complexity regions; Scoring matrix = PAM30; ITS Job ID = 14957398; LSU Job ID = 14957349). For rpb2, default BLAST settings were used (blastn; assembly database; Expect = 1*10-5; Word size = 11; Filter low complexity regions; Scoring matrix = BLOSUM62; rpb2 Job ID = 14957357). The best scoring sequence from theS. paradoxa KUC8140 strain genome for each region was extracted and downloaded. Raw sequence data were processed and assembled with Geneious version 9.0.2. (Kearse et al. 2012). Two individual datasets, ITS-LSU concatenated and rpb2, were created to compare the KUC8140 strain with other Xylodon species. The combination of novel, GenBank and KUC8140 sequences for each dataset were aligned in Geneious 9.0.2 with the MAFFT nucleotide sequence alignment function (Katoh and Standley 2013). The automatic alignments were reviewed manually through Geneious 9.0.2. Phylogenetic tree estimation for each alignment was performed using Maximum Likelihood (ML) and Bayesian Inference (BI). ML and bootstrapping analyses were conducted in RAxML (Stamatakis 2006), using default parameters established in the 124 Javier Fernández-López et al. / MycoKeys 38: 121–127 (2018) CIPRES web portal (http://www.phylo.org/portal2/; Miller et al. 2010) and calculat- ing bootstrap statistics from 1000 replicates. Bayesian inference analyses were imple- mented in BEAST v2.4.3 (Drummond and Rambaut 2007). Site model partition was selected using jModelTest2 (Darriba et al. 2012) and defined using BEAUti v2.4.3 interface. HKY and GTR substitution models were selected for ITS+LSU and rpb2 alignments, respectively, as the closest available in BEAST from the results obtained in jModelTest2. We used relative timing with an uncorrelated lognormal
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